Nucleic Acids Res 30(1): 186-190

PALS db: Putative Alternative Splicing database

^{Bioinformatics Program,}^{Institute of Biochemistry,}^{Bioinformatics Center and}^{Department of Life Sciences, National Yang-Ming University, No. 155, Sec. 2, Li-Noun Street, Taipei, Taiwan 11221, Republic of China}

^{To whom correspondence should be addressed. Tel: +886 2 2826 7128; Fax: +886 2 2826 4843; Email: yang@ym.edu.tw}

Received 2001 Sep 6; Revised 2001 Oct 31; Accepted 2001 Oct 31.

Abstract

PALS db is a collection of Putative Alternative Splicing information from 19 936 human UniGene clusters and 16 615 mouse UniGene clusters. Alternative splicing (AS) sites were predicted by using the longest messenger RNA (mRNA) sequence in each UniGene cluster as the reference sequence. This sequence was aligned with related sequences in UniGene and dbEST to reveal the AS. This information was presented with six features: (i) literature aliases were used to improve the result of a gene name search; (ii) the quality of a prediction can be easily judged from the color-coded similarity and the scaled length of an alignment; (iii) we have clustered those EST sequences that support the same AS site together to enhance the users’ confidence on a prediction; (iv) the users can also set up the alignment criteria interactively to recover false negatives; (v) tissue distribution can be displayed by placing the mouse cursor over an alignment; (vi) gene features will be analyzed at foreign sites by submitting the selected mRNA or its encoded protein as a query. Using these features, the users cannot only discover putative AS sites in silico, but also make new observations by combining AS information with tissue distributions or with gene features. PALS db is available at http://palsdb.ym.edu.tw/.

Abstract

ACKNOWLEDGEMENTS

Y.-H.H. and Y.-T.C. were supported by grants from National Science Council, Taiwan (NSC 89-2323-B-010-003 and NSC 89-2318-B-010-011-M51, respectively). S.-T.Y. was supported by a grant from Veterans General Hospital, Tsing-Hua University and Yang-Ming University (VTY90-P5-40). The computational resource was supported by Ministry of Education, ROC (Program for Promoting Academic Excellence of Universities, 89-B-FA22-2-4).

ACKNOWLEDGEMENTS

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